Amid the chaos of Guatemala City's evening rush hour, a grieving father sits motionless on a concrete bench beside a main road. On New Year's Day his seven-year-old daughter was killed. She had been sent out to buy a nappy for her baby brother but never arrived home - hours later her decapitated body was found in one of the deep gullies that run through the capital's slums.

"They called me to identify the body," says the 29-year-old hospital maintenance worker, who asks not to be named for fear of reprisals. "Then we took my little girl to the morgue."

His story is not unusual. Since 2001, more that 2,600 Guatemalan women and girls have been killed and the numbers seem to be accelerating - 110 were murdered in January and February this year alone. Only a negligible number of their killers has ever been convicted.

Last month a thousand activists marched through the fume-choked capital's centre, in a noisy protest at violence against women. Organisers said the turnout was larger and the participants more boisterous than they have ever been before. Human rights organisations, including Amnesty International, have been campaigning on this issue for years and, along with the killings in the Mexican border city of Ciudad Juárez, this represents one of Latin America's most pressing human rights emergencies.

When discussing these crimes it is necessary to put them in context - Guatemala is seeing a general explosion of violence, and 10 times as many men as women are killed each year. The murder of women wouldn't be a specific area of concern, then, if activists were not convinced that they are dying in a very different way. They call it femicide, claiming that while male victims are much more likely to die because they get involved in disputes, or join violent groups, women are being targeted in unprovoked attacks. And, they add, even women who expose themselves to risk by joining the ultra-violent gangs known as "maras" tend to be killed with a sadism not usually suffered by men.

"Many more men die, it's true, but women are being killed because they are women," says Sandra Morán, spokeswoman for a network of like-minded groups called The Women's Sector. Morán identifies several different types of killer, who, she claims, are united by a desire to mutilate women. They might be jilted lovers out for revenge, maras who target a rival by attacking his wife or girlfriend, or former soldiers and guerrillas who have found a new playground for their gruesome techniques.

She emphasises the latter, echoing a hypothesis popular among activists - that much of today's violence is rooted in the country's 36-year armed conflict, which ended in a peace accord signed a decade ago.

The war was one of Latin America's bloodiest, leaving 200,000 people dead. It was a bitter struggle between leftwing guerrillas and a military protecting a white elite and it resulted in hundreds of massacres, mostly carried out by the military, with unarmed civilians being slaughtered with a terrifying degree of cruelty.

Women made up about a quarter of the dead, and rape was common, while soldiers or paramilitaries also devised less obvious tortures, such as cutting foetuses (or, as they saw them, potential rebels) from the wombs of victims.

"We see the violence against women today as a continuum of the violence during the war," says Morán. She points to evidence that death squads associated with organised crime (and probably rooted in political repression) have penetrated deep into the postwar Guatemalan state. In February, four high-level policemen, arrested in connection with the murder of three Salvadorean politicians, were themselves killed by gunmen who breezed through eight locked doors to get to their cells. "If they can do that, then how much more easily can they torture and kill a woman?"

Rosa Franco's 15-year-old daughter disappeared on her way home from work five years ago. She was found in a ditch, badly beaten, stabbed in the chest, tied up with barbed wire and killed by a blow to the head. The first Franco knew about it was when she saw the image of her mutilated daughter on TV.

Sitting in her tiny living room, surrounded by photographs of her daughter in a frilly party frock, Franco says she still needs sleeping pills to switch off at night. "I just can't stop thinking of what she suffered," she says.

Franco has spent a great deal of time hassling the authorities to investigate her daughter's murder, even doing some detective work herself, following leads from a list of calls made to and from her daughter's mobile. Together with an eye-witness account of the body being dumped, Franco believes that she has tracked down the residence where - at the very least - her daughter was taken shortly before she was killed.

"I told the police and they said they went to look at the house, but that there was no one living there. That is a lie, because I have seen the cars come and go," says Franco, who believes her daughter was killed by a criminal boss with the connections necessary to ensure the investigation gets nowhere. She is also convinced that this explains the series of menacing vehicles that regularly used to lurk near her house, and the men on bicycles who would pedal slowly behind her two sons as they walked to school.

Carla Villagrán, from the Human Rights Ombudsman's office, heads the most thorough investigation yet of the murders - a painstaking revision of three years of police files from 2003 to 2005. So far, she says, the files have failed to confirm that women are being killed because of their gender.

There has recently been a rise in the proportion of female murder victims in the country, from about 8% to 10% of the total, but this is hardly enough proof. There are also more cases of female victims suffering mutilation, but the files do little more than note this fact. And while there is much anecdotal evidence of rape associated with murder, the vast majority of autopsies don't even bother to check. "In Guatemala we still do not know if there is a phenomenon of femicide or not," says Villagrán. "The quality of the police investigations is too poor to tell."

Most activists in Guatemala or abroad feel no need for formal confirmation. Adriana Beltrán, of the Washington Office of Latin America (a US-based human rights group which, last month, published a special report on the death of women in Guatemala) says part of the problem is that Guatemala's legal framework is still deeply sexist. It was not until last year, she points out, that a law permitting a rapist to escape charges by marrying the victim was abolished, and other discriminatory laws are still in place. Police, prosecutors and judges are hardly known for their liberal attitudes, either, as they are prone to hinting that a young woman's murder can be explained by the length of her skirt.

One morning recently, in front of three judges, bereaved father Carlos Pac answered questions about the kidnap, rape and murder of his 20-year-old daughter three years ago. The defence lawyer began asking if his daughter was in the habit of coming home late.

"Never, never," his wife murmured in the public gallery, fiddling furiously with a rosary. "She was a good girl. A good student, a good girl."

The Pacs' combination of relative wealth, education and determination to see the case through makes them uncommon among victims' families. In pursuing the case, they also had to muster the courage to ignore two grenade attacks on the family home. "This is just something we have to do," Carlos Pac told me, during a recess in proceedings that was expected to last for several weeks. He added that he believed there were other members of the kidnapping gang at large who he was also determined to bring to justice.

Less than 1% of all criminal cases ever reach the sentencing stage, with fear that the killers will exact revenge cited as one of the main reasons that so many investigations fail. Women's activists say that fear is also one of the main problems they face as they try to galvanise people inside Guatemala to pressure the government to do more.

Some government initiatives have been welcomed - such as the creation of a special prosecutor's office for violence against women in 2005, and a specialised commission to study the issue in 2006. They have also sometimes been disappointing - the special prosecutor's office no longer handles murders, and the commission has yet to do anything significant.

As the buses thunder past, the father of the seven-year-old girl killed on New Year's Day says that he and his wife have decided to let the case drop and to stop talking to journalists.

"There's no point," he says as our interview draws to a close. Within minutes he has disappeared into the evening stampede of people, all desperate to get home before dark.

· Amnesty International is holding a speakers' tour during May - visiting London, Edinburgh and Belfast - in which campaigners from Guatemala and Mexico will be telling their stories about seeking justice for women.